Effect of ionic charge on OH⋯Se hydrogen bond: A computational study

Importance of water and intramolecular interaction governs substantial blue shift of Csp2–H stretching frequency in complexes between chalcogenoaldehydes and water

Geometrical structure, stability and cooperativity, and contribution of hydrogen bonds to the stability of complexes between chalcogenoaldehydes and water were thoroughly investigated using quantum chemical methods. The stability of the complexes increases significantly when one or more H₂O molecules are added to the binary system, whereas it decreases sharply going from O to S, Se, or Te substitution. The O–H⋯O H-bond is twice as stable as C_sp²–H⋯O and O–H⋯S/Se/Te H-bonds. It is found that a considerable blue-shift of C_sp²–H stretching frequency in the C_sp²–H⋯O H-bond is mainly determined by an addition of water into the complexes along with the low polarity of the C_sp²–H covalent bond in formaldehyde and acetaldehyde. The C_sp²–H stretching frequency shift as a function of net second hyperconjugative energy for the σ*(C_sp²–H) antibonding orbital is observed. Remarkably, a considerable C_sp²–H blue shift of 109 cm⁻¹ has been reported for the first time. Upon the addition of H₂O into the binary systems, halogenated complexes witness a decreasing magnitude of the C_sp²–H stretching frequency blue-shift in the C_sp²–H⋯O H-bond, whereas CH₃-substituted complexes experience the opposite trend.

The considerable blue shift of C_sp²–H stretching frequency.

Participation of S and Se in hydrogen and chalcogen bonds

The heavier chalcogen atoms S, Se, and Te can each participate in a range of different noncovalent interactions. They can serve as both proton donor and acceptor in H-bonds. Each atom can also act as electron acceptor in a chalcogen bond.

Supramolecular insight into the substitution of sulfur by selenium, based on crystal structures, quantum-chemical calculations and biosystem recognition

Statistical analysis of data from crystal structures extracted from the Cambridge Structural Database (CSD) has shown that S and Se atoms display a similar tendency towards specific types of interaction if they are part of a fragment that corresponds to the side chains of cysteine (Cys), methionine (Met) selenocysteine (Sec) and selenomethionine (Mse). The most numerous are structures with C-H...Se and C-H...S interactions (∼80%), notably less numerous are structures with Se...Se and S...S interactions (∼5%), and Se...π and S...π interactions are the least numerous. The results of quantum-chemical calculations have indicated that C-H...Se (∼-0.8 kcal mol^-1) and C-H...S interactions are weaker than the most stable parallel interaction (∼-3.3 kcal mol^-1) and electrostatic interactions of σ/π type (∼-2.6 kcal mol^-1). Their significant presence can be explained by the abundance of CH groups compared with the numbers of Se and S atoms in the crystal structures, and also by the influence of substituents bonded to the Se or S atom that further reduce their possibilities for interacting with species from the environment. This can also offer an explanation as to why O-H...Se (∼-4.4 kcal mol^-1) and N-H...Se interactions (∼-2.2 kcal mol^-1) are less numerous. Docking studies revealed that S and Se rarely participate in interactions with the amino acid residues of target enzymes, mostly because those residues preferentially interact with the substituents bonded to Se and S. The differences between Se and S ligands in the number and positions of their binding sites are more pronounced if the substituents are polar and if there are more Se/S atoms in the ligand.

Thioamide, a Hydrogen Bond Acceptor in Proteins and Nucleic Acids

Thioamides are used as potential surrogates of amides to study the structure and dynamics of proteins and nucleic acids. However, incorporation of thioamides in biomolecules leads to changes in their structures and conformations mostly attributed to the strength of the amide-N-H···S═C hydrogen bond. In most cases, it is considered weak owing to the small electronegativity of sulfur, and in some cases, it is as strong as conventional H-bonds. Herein, adopting PDB structure analysis, NMR spectroscopy, and quantum chemistry calculations, we have shown that thioamides in a geometrical and structural constraint-free environment are capable of forming strong H-bonds like their amide counterparts. These studies also enabled us to determine the amide-N-H···S═C H-bond enthalpy (ΔH) very precisely. The estimated ΔH for the amide-N-H···S═C H-bond is ∼-30 kJ/mol, which suggests that the amide-N-H···S═C H-bond is a strong H-bond and merits its inclusion in computational force fields for biomolecular structure simulations to explore the role of amide-N-H···S═C H-bonds in nucleobase pairing and protein folding.